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Missing required dependencies ['numpy'] #6

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rusalkaguy opened this issue May 12, 2020 · 0 comments
Open

Missing required dependencies ['numpy'] #6

rusalkaguy opened this issue May 12, 2020 · 0 comments

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@rusalkaguy
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snakemake/5.9.1 requires GCCcore-7.3.0

dvctools/1.4 requires GCCcore-5.4.0

If dvctools is loaded 2nd, then module, for some reason, downgrades GCCcore, and snakemake fails.

If dvctools is loaded 1st, then it seems to work well with GCCcore-7.3.0, and life is good.

[last: 0s][~]$ module load snakemake/5.9.1-foss-2018b-Python-3.6.6
[last: 1s][~]$ module list

Currently Loaded Modules:
  1) shared                        9) numactl/2.0.11-GCCcore-7.3.0                17) bzip2/1.0.6-GCCcore-7.3.0      25) Python/3.6.6-foss-2018b
  2) slurm/18.08.9                10) hwloc/1.11.10-GCCcore-7.3.0                 18) ncurses/6.1-GCCcore-7.3.0      26) libyaml/0.2.1-GCCcore-7.3.0
  3) rc-base                      11) OpenMPI/3.1.1-GCC-7.3.0-2.30                19) libreadline/7.0-GCCcore-7.3.0  27) PyYAML/3.13-foss-2018b-Python-3.6.6
  4) DefaultModules               12) OpenBLAS/0.3.1-GCC-7.3.0-2.30               20) Tcl/8.6.8-GCCcore-7.3.0        28) GitPython/2.1.11-foss-2018b-Python-3.6.6
  5) GCCcore/7.3.0                13) gompi/2018b                                 21) SQLite/3.24.0-GCCcore-7.3.0    29) snakemake/5.9.1-foss-2018b-Python-3.6.6
  6) binutils/2.30-GCCcore-7.3.0  14) FFTW/3.3.8-gompi-2018b                      22) XZ/5.2.4-GCCcore-7.3.0
  7) GCC/7.3.0-2.30               15) ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1  23) GMP/6.1.2-GCCcore-7.3.0
  8) zlib/1.2.11-GCCcore-7.3.0    16) foss/2018b                                  24) libffi/3.2.1-GCCcore-7.3.0



[last: 0s][~]$ module load dvctools

The following have been reloaded with a version change:
  1) GCC/7.3.0-2.30 => GCC/5.4.0-2.26     2) GCCcore/7.3.0 => GCCcore/5.4.0     3) binutils/2.30-GCCcore-7.3.0 => binutils/2.26-GCCcore-5.4.0

[last: 1s][~]$ cd scratch/zajac/rna.sm524-2/
[last: 0s][~/scratch/zajac/rna.sm524-2]$ snakemake -n
ImportError in line 1 of /scratch/curtish/zajac/rna.sm524-2/Snakefile:
Missing required dependencies ['numpy']
  File "/scratch/curtish/zajac/rna.sm524-2/Snakefile", line 1, in <module>
  File "/share/apps/rc/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/pandas-0.23.4-py3.6-linux-x86_64.egg/pandas/__init__.py", line 19, in <module>
[last: 1s][~/scratch/zajac/rna.sm524-2]$
rusalkaguy added a commit that referenced this issue May 12, 2020
Also start loading dvctools first, to avoid GCC conflicts caused when it's loaded 2nd.
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